The prosecution of Mr. Kiriakou is the sixth criminal case brought under President Obama against current or former government officials accused of providing classified information to the media, more such cases than all previous presidents combined. The crackdown, long sought by the C.I.A. and other agencies, has won the administration some credit with security officials angered by the president’s earlier decision to release classified legal opinions on the agency’s interrogation program.

Officials have said the administration’s campaign against leaks has resulted from a belief among the intelligence agencies and members of both parties in Congress that unauthorized disclosures by government employees holding security clearances were out of control. But Mr. Obama entered office pledging unprecedented transparency for government operations, and his record has drawn fire from civil libertarians and groups supporting whistle-blowers and press freedoms.

Among other things, the F.B.I. complaint accuses Mr. Kiriakou of being a source for a June 2008 front-page Times article, written by reporter Scott Shane. It identified a C.I.A. employee, Deuce Martinez, who played a major role interrogation of Abu Zubaydah, believed to have handled logistics for Al Qaeda, and Khalid Shaikh Mohammed, the self-described mastermind of the Sept. 11 attacks.

Robert Christie, a spokesman for The Times, declined to comment.

The case is the second against a former C.I.A. officer for allegedly disclosing classified information to reporters within the past year. In 2011, Jeffrey Sterling, a former agency employee, was charged with leaking information allegedly used by James Risen, a Times reporter, in his 2006 book, “State of War.” (That case may be collapsing due to a judge’s ruling barring two witnesses from testifying; the prosecution has appealed.)

In a statement on Monday warning C.I.A. employees not to leak information, the C.I.A. director, David H. Petraeus, took note of both cases, saying that the agency “fully supported the investigation from the beginning and will continue to do so.”

The agency had initially pressed for an investigation of the Guantánamo detainee lawyers — not of its own former employee. The inquiry traces back to the spring of 2009, after government officials learned that Guantánamo defense lawyers were trying to identify C.I.A. interrogators — including the discovery of 32 pages of photographs in the cells of several Guantánamo detainees. The photos were a line-up of random people and suspected interrogators; the attorneys were trying to identify potential witnesses who could testify about abusive treatment, as mitigating evidence against death sentences.

That discovery led to an uproar within the C.I.A., where critics feared the move could put officials involved in the interrogation program at risk. The agency pressed for a criminal investigation, and Mr. Holder eventually appointed Patrick J. Fitzgerald, a United States attorney who led a high-profile C.I.A. leak investigation during the Bush administration, to handle it.